plotMotifLogo: plot sequence logo

View source: R/plotMotifLogo.R

plotMotifLogoR Documentation

Description

plot amino acid or DNA sequence logo

Usage

plotMotifLogo(
  pfm,
  motifName,
  p = rep(0.25, 4),
  font = "sans",
  fontface = "bold",
  colset = c("#00811B", "#2000C7", "#FFB32C", "#D00001"),
  xaxis = TRUE,
  yaxis = TRUE,
  xlab = "position",
  ylab = "bits",
  xlcex = 1.2,
  ylcex = 1.2,
  ncex = 1.2,
  ic.scale = TRUE,
  newpage = TRUE,
  margins = c(4.1, 4.1, 2.1, 0.1),
  draw = TRUE,
  ...
)

Arguments

pfm

a position frequency matrices

motifName

motif name

p

background possibility

font

font of logo

fontface

fontface of logo

colset

color setting for each logo letter

xaxis

draw x-axis or not. If a vector of character or numeric is provided, the function will try to plot the x-axis by setting the labels as the vectors.

yaxis

draw y-axis or not

xlab

x-label, do nothing if set xlab as NA

ylab

y-label, do nothing if set ylab as NA

xlcex

cex value for x-label

ylcex

cex value for y-label

ncex

cex value for motif name

ic.scale

logical If TRUE, the height of each column is proportional to its information content. Otherwise, all columns have the same height. It will also can be set as FALSE followed by a numeric vectors. The format is c(FALSE, scale). If it is FALSE followed by a number (eg c(FALSE, 100)), the y axis labels will be re-scaled by 100.

newpage

logical If TRUE, plot it in a new page.

margins

A numeric vector interpreted in the same way as par(mar) in base graphics.

draw

Vector (logical(1)). TRUE to plot. FALSE, return a gList

...

Not used.

Value

none

Examples


pcm<-matrix(runif(40,0,100),nrow=4,ncol=10)
pfm<-pcm2pfm(pcm)
rownames(pfm)<-c("A","C","G","T")
plotMotifLogo(pfm)


jianhong/motifStack documentation built on Nov. 5, 2024, 7:47 a.m.